Pretty pictures, but I still don't get why you want to scale down the surface, then scale it back up.
I could see lying to a volume header, or resampling the anatomical, to get SureFit to behave better. And if you do that, you would need to rescale the surface to get rid of the deliberately mis-stated resolution in the volume header. On Aug 26, 2012, at 6:43 PM, Colin Reveley wrote: > > I don't think it makes sense at in human, or rhesus. > > however in marmoset the caudal white matter (which is really most of the > white matter) is arranged in a sort of nested shell type deal. the inner > white matter is the most myelinated, mainly its seems mostly the optic > radation. but not only that. > > the principle diffusoion direction of the outer shell seems orthogonal to the > inner. and there is a very clear boundary. > > so one might want to map DTI maps, FA and etc etc between these shells to > characterise the WM. > > here are a couple of picture at 100um showing what I mean. > > it can only possibly work when the anatomy is like this, and also no folding > > probably not even then > > but if it did work I can map ev's, vol ratio, myelin, lattice index, loads of > measures. and hence learn more about marmoset anatomy. > > which is a new thing for me. there's nearly nothing on its WM structure in > the literature. I'm trying to figure it out. > > It's an idea. no more. > > On 25 August 2012 18:00, <[email protected]> wrote: > Send caret-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: Inner white matter (Donna Dierker) > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" <[email protected]> > Cc: > Date: Fri, 24 Aug 2012 13:17:17 -0500 > Subject: Re: [caret-users] Inner white matter > Go here: > > http://www.nitrc.org/frs/download.php/2871/GIFTI_Surface_Format.pdf > > On page 36, it says: The application of a CoordinateSystemTransformMatrix, > places the coordinates into the system shown in the table below. All > coordinates are in millimeters. > > So sorry: You don't get to change units. > > But I know I'm not the only one scratching my head wondering why you want to > do this. Oh, I know the occasional temptation to lie in a volume header, to > elicit certain software behavior. > > But I've never been tempted to do it on a surface. I've scaled surfaces for > real (e.g., if I had to lie in a header when segmenting a smaller mammal, to > get SureFit to do the right thing). But not to get surfaces to behave > properly. So I guess I'm curious. > > Because what you describe below seems to me to be the equivalent of taking > x,y,z axes; lining out the indices and writing numbers 1/4 the size of the > original marks; and then lining those through and writing the original marks > down. Which means I'm almost certainly not getting what you asked. > > > On Aug 24, 2012, at 1:47 AM, Colin Reveley wrote: > > > Would it be possible to shrink a surface with a scaling matrix, and then > > define the mesh as being in the same space as the original. > > > > E.g a mesh at 1mm scaled down to eg 0.25mm and then redefined as a 1mm > > surface? > > > > The notion here is to generate an outer and inner pair of white matter > > surfaces. Of course there are issues. > > > > The general notion is to then treat these as white and pial surfaces, take > > their mean and map white matter data using matt's method for mapping gray > > matter data (scalar diffusion maps). > > > > This is less nuts than it sounds in marmoset because the white matter is > > simple topologically and in terms of gross anatomy , particularly in the > > caudal half of the brain. > > > > In principle there should be a mid thickness line in much of the brains > > white matter. > > > > With a nifti you just change the units in the header. I don't appear to see > > a gifti equivalent. > > > > Thanks > > > > Colin > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > <d1_f1_occip.png><f1_occip_3class.png>_______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
